tests/testthat/test_simData.R

In bmcclintock/momentuHMM: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models

context("simData")

test_that("Exceptions are thrown",{
  stepPar <- c(1,10,1,5,0.2,0.3)
  anglePar <- c(0,pi,0.5,2)

  expect_error(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              NA)
  expect_error(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar[1:4],angle=anglePar),nbCovs=2),
              NA)
  expect_error(simData(1,2,dist=list(omega="beta",angle="vm"),Par=list(omega=stepPar,angle=anglePar),nbCovs=2,oneInflation=list(omega=TRUE)),
               NA)
  expect_error(simData(1,2,dist=list(omega="beta",angle="vm"),Par=list(omega=c(stepPar,0.05,0.01),angle=anglePar),nbCovs=2,zeroInflation=list(omega=TRUE),oneInflation=list(omega=TRUE)),
               NA)
  expect_error(simData(1,2,dist=list(step="gamma",omega="beta",angle="vm"),Par=list(step=stepPar,omega=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE),oneInflation=list(omega=TRUE)),
               NA)
  expect_error(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar[1:4],angle=anglePar),spatialCovs=list(forest=forest),obsPerAnimal=250),
               NA)
  expect_error(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar[1:4],angle=anglePar),centers=matrix(c(0,500,0,500),2,2),obsPerAnimal=250),
               NA)

  expect_that(simData(0,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error("nbAnimals should be at least 1."))
  expect_that(simData(1,0,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error("nbStates should be at least 1."))

  expect_that(simData(1,2,dist=list(step="norm",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  expect_that(simData(1,2,dist=list(step="norm",angle="norm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  expect_that(simData(1,2,dist=list(step="vm",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  expect_that(simData(1,2,dist=list(step="gamma",angle="weibull"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())

  stepPar2 <- c(stepPar,1)
  expect_that(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar2,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  anglePar2 <- c(anglePar,1)
  expect_that(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar2),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())

  stepPar <- c(-1,10,1,5,0.2,0.3)
  expect_that(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  stepPar <- c(1,10,1,-0.5,0.2,0.3)
  expect_that(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
  stepPar <- c(1,10,1,5,4,0.3)
  expect_that(simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE)),
              throws_error())
})

test_that("The right slots are defined",{
  stepPar <- c(1,10,1,5,0.2,0.3)
  anglePar <- c(0,pi,0.5,2)
  nbCovs <- 2
  data <- simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE))

  expect_true(!is.null(data$ID))
  expect_true(!is.null(data$x))
  expect_true(!is.null(data$y))
  expect_true(!is.null(data$step))
  expect_true(!is.null(data$angle))

  expect_equal(length(which(names(data)!="ID" & names(data)!="x" & names(data)!="y" &
                              names(data)!="step" & names(data)!="angle")),nbCovs)
})

test_that("The returned object is of the correct class",{
  stepPar <- c(1,10,1,5,0.2,0.3)
  anglePar <- c(0,pi,0.5,2)
  data <- simData(1,2,dist=list(step="gamma",angle="vm"),Par=list(step=stepPar,angle=anglePar),nbCovs=2,zeroInflation=list(step=TRUE))

  expect_equal(class(data),c("momentuHMMData","data.frame"))
})

test_that("Data can be simulated with observation error from existing model",{
  m<-example$m
  obsPerAnimal<-c(50,100)
  lambda <- 2 # expect 2 observations per time step
  errorEllipse <- list(M=50,m=25,r=180)
  expect_error(simData(model=m,obsPerAnimal=obsPerAnimal,lambda=lambda, errorEllipse=errorEllipse),
               NA)
})